The Mouse Phenome Database (MPD) provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD ensures rigorous curation of phenotype data and supporting documentation using relevant ontologies and controlled vocabularies. As a repository of curated and integrated data, MPD provides a means to access/re-use baseline data, as well as allows users to identify sensitized backgrounds for making new mouse models with genome editing technologies, analyze trait co-inheritance, benchmark assays in their own laboratories, and many other research applications. MPD’s primary source of funding is NIDA. For this reason, a majority of MPD data is neuro- and behavior-related.
This opening lecture from INCF's Short Course in Neuroinformatics provides an overview of the field of neuroinformatics itself, as well as laying out an argument for the necessity for developing more sophisticated approaches towards FAIR data management principles in neuroscience.
This lesson continues from part one of the lecture Ontologies, Databases, and Standards, diving deeper into a description of ontologies and knowledg graphs.
This lesson aims to define computational neuroscience in general terms, while providing specific examples of highly successful computational neuroscience projects.
This lecture covers a wide range of aspects regarding neuroinformatics and data governance, describing both their historical developments and current trajectories. Particular tools, platforms, and standards to make your research more FAIR are also discussed.
Presented by the OHBM OpenScienceSIG, this lesson covers how containers can be useful for running the same software on different platforms and sharing analysis pipelines with other researchers.
Serving as good refresher, this lesson explains the maths and logic concepts that are important for programmers to understand, including sets, propositional logic, conditional statements, and more.
This compilation is courtesy of freeCodeCamp.
This lesson provides a useful refresher which will facilitate the use of Matlab, Octave, and various matrix-manipulation and machine-learning software.
This lesson was created by RootMath.
This lecture provides an introduction to the study of eye-tracking in humans.
This is a hands-on tutorial on PLINK, the open source whole genome association analysis toolset. The aims of this tutorial are to teach users how to perform basic quality control on genetic datasets, as well as to identify and understand GWAS summary statistics.
This lesson is an overview of transcriptomics, from fundamental concepts of the central dogma and RNA sequencing at the single-cell level, to how genetic expression underlies diversity in cell phenotypes.
In this third and final hands-on tutorial from the Research Workflows for Collaborative Neuroscience workshop, you will learn about workflow orchestration using open source tools like DataJoint and Flyte.
In this hands-on session, you will learn how to explore and work with DataLad datasets, containers, and structures using Jupyter notebooks.
This lecture describes how to build research workflows, including a demonstrate using DataJoint Elements to build data pipelines.
This video will document the process of uploading data into a brainlife project using ezBIDS.
This short video walks you through the steps of publishing a dataset on brainlife, an open-source, free and secure reproducible neuroscience analysis platform.
This video will document the process of visualizing the provenance of each step performed to generate a data object on brainlife.
This video will document the process of downloading and running the "reproduce.sh" script, which will automatically run all of the steps to generate a data object locally on a user's machine.
This video will document the process of creating a pipeline rule for batch processing on brainlife.
This short video shows how a brainlife.io publication can be opened from the Data Deposition page of the journal Nature Scientific Data.